geneOntology.c File Reference

Gene Ontology (GO) routines. More...

#include "log.h"
#include "format.h"
#include "linestream.h"
#include "geneOntology.h"
#include <gsl/gsl_randist.h>

Go to the source code of this file.

Functions

Array geneOntology_calculateGeneDepletion (Array goNodePointers, int multipleTestingCorrectionMethod)

Calculate the gene depletion for every GoNode in goNodePointers.

Array geneOntology_calculateGeneEnrichment (Array goNodePointers, int multipleTestingCorrectionMethod)

Calculate the gene enrichment for every GoNode in goNodePointers.

GoGeneAssociation * geneOntology_findGoGeneAssociation (char *geneName)

Find a GoGeneAssociation.

GoNode * geneOntology_findGoNode (char *id)

Find a GoNode.

Array geneOntology_getAllGoNodes (void)

Get the GoNodes of the entire ontology.

Array geneOntology_getBiologicalProcessGoNodes (void)

Get the GoNodes that are part of the biological_process hierarchy.

GoNode * geneOntology_getBiologicalProcessRoot (void)

Get the GoNode that points to the biological_process root.

Array geneOntology_getCellularComponentGoNodes (void)

Get the GoNodes that are part of the cellular_component hierarchy.

GoNode * geneOntology_getCellularComponentRoot (void)

Get the GoNode that points to the cellular_component root.

Array geneOntology_getChildrenAtSpecifiedHierarchyLevel (GoNode *currGoNode, int level)

Get the children of a GoNode at a specified hiearchy level.

Array geneOntology_getGenericGoSlimNodes (void)

Get the generic GO slim nodes.

Array geneOntology_getMolecularFunctionGoNodes (void)

Get the GoNodes that are part of the molecular_function hierarchy.

GoNode * geneOntology_getMolecularFunctionRoot (void)

Get the GoNode that points to the molecular_function root.

int geneOntology_getNumberOfAssociatedGenes (void)

Get the number of associated genes.

int geneOntology_getNumberOfGenesOfInterest (void)

Get the number of genes of interest that have been mapped to the gene ontology.

void geneOntology_init (char *geneOntologyFileName)

Initialize the geneOntology module.

void geneOntology_mapGeneAnnotationsToGeneOntology (char *goGeneAssociationFileName)

Map gene annotations to the gene ontology.

Texta geneOntology_mapGenesOfInterestToGeneOntology (Texta geneNamesOfInterest)

Map genes of interest to the gene ontology.

void geneOntology_resetGenesOfInterest (void)

Resets (performs arrayClear()) the genes of interest for every GoNode.

Detailed Description

Gene Ontology (GO) routines.

Note this module depends on the GNU scientific library (http://www.gnu.org/software/gsl).

Author:: Lukas Habegger (lukas.habegger@yale.edu)

Definition in file geneOntology.c.

Function Documentation

Array geneOntology_calculateGeneDepletion	(	Array	goNodePointers,
		int	multipleTestingCorrectionMethod
	)

Calculate the gene depletion for every GoNode in goNodePointers.

Parameters:

`[in]`	goNodePointers	Array of goNode pointers. Gene depletion is calculated for every goNode in this Array.
`[in]`	multipleTestingCorrectionMethod	Specifies the multiple testing correction method. Use either MULTIPLE_TESTING_CORRECTION_BENJAMINI_HOCHBERG or MULTIPLE_TESTING_CORRECTION_BONFERRONI.

Returns:: Array of type GoStatistic. This array is sorted by pvalue in ascending order.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 822 of file geneOntology.c.

Array geneOntology_calculateGeneEnrichment	(	Array	goNodePointers,
		int	multipleTestingCorrectionMethod
	)

Calculate the gene enrichment for every GoNode in goNodePointers.

Parameters:

`[in]`	goNodePointers	Array of goNode pointers. Gene enrichment is calculated for every goNode in this Array.
`[in]`	multipleTestingCorrectionMethod	Specifies the multiple testing correction method. Use either MULTIPLE_TESTING_CORRECTION_BENJAMINI_HOCHBERG or MULTIPLE_TESTING_CORRECTION_BONFERRONI.

Returns:: Array of type GoStatistic. This array is sorted by pvalue in ascending order.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 802 of file geneOntology.c.

GoGeneAssociation* geneOntology_findGoGeneAssociation ( char * geneName )

Find a GoGeneAssociation.

Parameters:

[in] geneName A geneName or geneSymbol as specified in the geneAssociation file. See http://www.geneontology.org/GO.format.annotation.shtml for details. This geneName refers to the third column labeled as DB_Object_Symbol.

Returns:: A pointer to the GoGeneAssociation, NULL if GoGeneAssociation was not found

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 554 of file geneOntology.c.

GoNode* geneOntology_findGoNode ( char * id )

Find a GoNode.

Parameters:

[in] id A GO term identifier. Example: GO:0065003

Returns:: A pointer to the GoNode, NULL if the GO term was not found

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 365 of file geneOntology.c.

Array geneOntology_getAllGoNodes ( void )

Get the GoNodes of the entire ontology.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 143 of file geneOntology.c.

Array geneOntology_getBiologicalProcessGoNodes ( void )

Get the GoNodes that are part of the biological_process hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 107 of file geneOntology.c.

GoNode* geneOntology_getBiologicalProcessRoot ( void )

Get the GoNode that points to the biological_process root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 47 of file geneOntology.c.

Array geneOntology_getCellularComponentGoNodes ( void )

Get the GoNodes that are part of the cellular_component hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 131 of file geneOntology.c.

GoNode* geneOntology_getCellularComponentRoot ( void )

Get the GoNode that points to the cellular_component root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 71 of file geneOntology.c.

Array geneOntology_getChildrenAtSpecifiedHierarchyLevel	(	GoNode *	currGoNode,
		int	level
	)

Get the children of a GoNode at a specified hiearchy level.

Parameters:

`[in]`	currGoNode	Get the children of this GoNode at the specified hiearchy level.
`[in]`	level	Specifies the level within the gene ontology relative to the currGoNode. The level of currGoNode is 0. Example: To get the grand-children of currGoNode the level would be 2.

Returns:: An Array of GoNode pointers.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 868 of file geneOntology.c.

Array geneOntology_getGenericGoSlimNodes ( void )

Get the generic GO slim nodes.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Note:: The memory belongs to this module

Definition at line 156 of file geneOntology.c.

Array geneOntology_getMolecularFunctionGoNodes ( void )

Get the GoNodes that are part of the molecular_function hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 119 of file geneOntology.c.

GoNode* geneOntology_getMolecularFunctionRoot ( void )

Get the GoNode that points to the molecular_function root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 59 of file geneOntology.c.

int geneOntology_getNumberOfAssociatedGenes ( void )

Get the number of associated genes.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 169 of file geneOntology.c.

int geneOntology_getNumberOfGenesOfInterest ( void )

Get the number of genes of interest that have been mapped to the gene ontology.

Note: duplicates gene names were removed.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 185 of file geneOntology.c.

void geneOntology_init ( char * geneOntologyFileName )

Initialize the geneOntology module.

Parameters:

[in] geneOntologyFileName File that describes the entire gene ontology. This file has to be in OBO format. See http://www.geneontology.org/GO.format.obo-1_2.shtml for details.

Definition at line 619 of file geneOntology.c.

void geneOntology_mapGeneAnnotationsToGeneOntology ( char * goGeneAssociationFileName )

Map gene annotations to the gene ontology.

Parameters:

[in] goGeneAssociationFileName File that maps the genes of a specific organism to the gene ontology. This file has to be in GO Annotation format. See http://www.geneontology.org/GO.format.annotation.shtml for details.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 633 of file geneOntology.c.

Texta geneOntology_mapGenesOfInterestToGeneOntology ( Texta geneNamesOfInterest )

Map genes of interest to the gene ontology.

Parameters:

[in] genesNamesOfInterest Texta that contains the gene names of the genes of interest. The gene names must be consistent with the genes names found in the gene annotation file.

Returns:: Texta of invalid gene names. If the number of invalid gene names is zero, then an empty Texta is returned.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 580 of file geneOntology.c.

void geneOntology_resetGenesOfInterest ( void )

Resets (performs arrayClear()) the genes of interest for every GoNode.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Postcondition:: A new set of genes of interest can be mapped to the gene ontology by using geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 202 of file geneOntology.c.


Functions
Array	geneOntology_calculateGeneDepletion (Array goNodePointers, int multipleTestingCorrectionMethod)
	Calculate the gene depletion for every GoNode in goNodePointers.
Array	geneOntology_calculateGeneEnrichment (Array goNodePointers, int multipleTestingCorrectionMethod)
	Calculate the gene enrichment for every GoNode in goNodePointers.
GoGeneAssociation *	geneOntology_findGoGeneAssociation (char *geneName)
	Find a GoGeneAssociation.
GoNode *	geneOntology_findGoNode (char *id)
	Find a GoNode.
Array	geneOntology_getAllGoNodes (void)
	Get the GoNodes of the entire ontology.
Array	geneOntology_getBiologicalProcessGoNodes (void)
	Get the GoNodes that are part of the biological_process hierarchy.
GoNode *	geneOntology_getBiologicalProcessRoot (void)
	Get the GoNode that points to the biological_process root.
Array	geneOntology_getCellularComponentGoNodes (void)
	Get the GoNodes that are part of the cellular_component hierarchy.
GoNode *	geneOntology_getCellularComponentRoot (void)
	Get the GoNode that points to the cellular_component root.
Array	geneOntology_getChildrenAtSpecifiedHierarchyLevel (GoNode *currGoNode, int level)
	Get the children of a GoNode at a specified hiearchy level.
Array	geneOntology_getGenericGoSlimNodes (void)
	Get the generic GO slim nodes.
Array	geneOntology_getMolecularFunctionGoNodes (void)
	Get the GoNodes that are part of the molecular_function hierarchy.
GoNode *	geneOntology_getMolecularFunctionRoot (void)
	Get the GoNode that points to the molecular_function root.
int	geneOntology_getNumberOfAssociatedGenes (void)
	Get the number of associated genes.
int	geneOntology_getNumberOfGenesOfInterest (void)
	Get the number of genes of interest that have been mapped to the gene ontology.
void	geneOntology_init (char *geneOntologyFileName)
	Initialize the geneOntology module.
void	geneOntology_mapGeneAnnotationsToGeneOntology (char *goGeneAssociationFileName)
	Map gene annotations to the gene ontology.
Texta	geneOntology_mapGenesOfInterestToGeneOntology (Texta geneNamesOfInterest)
	Map genes of interest to the gene ontology.
void	geneOntology_resetGenesOfInterest (void)
	Resets (performs arrayClear()) the genes of interest for every GoNode.